Life Sciences Commons^™

A Machine Learning Approach For Using The Postmortem Skin Microbiome To Estimate The Postmortem Interval, Hunter R. Johnson, Donovan D. Trinidad, Stephania Guzman, Zenab Khan, James V. Parziale, Jennifer M. Debruyn, Nathan H. Lents

Publications and Research

Research on the human microbiome, the microbiota that live in, on, and around the human person, has revolutionized our understanding of the complex interactions between microbial life and human health and disease. The microbiome may also provide a valuable tool in forensic death investigations by helping to reveal the postmortem interval (PMI) of a decedent that is discovered after an unknown amount of time since death. Current methods of estimating PMI for cadavers discovered in uncontrolled, unstudied environments have substantial limitations, some of which may be overcome through the use of microbial indicators. In this project, we sampled the microbiomes …

Comparative Phylogeography In The Atlantic Forest And Brazilian Savannas: Pleistocene Fluctuations And Dispersal Shape Spatial Patterns In Two Bumblebees, Elaine Françoso, Alexander Rizzo Zuntini, Ana Carolina Carnaval, Maria Cristina Arias

Publications and Research

Background: Bombus morio and B. pauloensis are sympatric widespread bumblebee species that occupy two major Brazilian biomes, the Atlantic forest and the savannas of the Cerrado. Differences in dispersion capacity, which is greater in B. morio, likely influence their phylogeographic patterns. This study asks which processes best explain the patterns of genetic variation observed in B. morio and B. pauloensis, shedding light on the phenomena that shaped the range of local populations and the spatial distribution of intra-specific lineages.

Results: Results suggest that Pleistocene climatic oscillations directly influenced the population structure of both species. Correlative species distribution models predict that …

Radiation Damage In Xfel: Case Study From The Oxygen-Evolving Complex Of Photosystem Ii, Muhamed Amin, Ashraf Badawi, S.S. Obayya

Publications and Research

Structural changes induced by radiation damage in X-ray crystallography hinder the ability to understand the structure/function relationship in chemical reactions. Serial femtosecond crystallography overcomes this problem by exposing the sample to very short and intense laser pulse leading to measurement before destruction. Here we use molecular modeling to map the radiation damage during the 10–50 fs to the intensity, the energy and the time duration of the laser pulse on the oxygen-evolving complex (OEC) of photosystem II. In the model, the nuclei move classically in a fully quantum potential created by electron density under the effect of strong laser pulse …

The Evolution Of Line-1 In Vertebrates, Stephane Boissinot, Akash Sookdeo

Publications and Research

The abundance and diversity of the LINE-1 (L1) retrotransposon differ greatly among vertebrates. Mammalian genomes contain hundreds of thousands L1s that have accumulated since the origin of mammals. A single group of very similar elements is active at a time in mammals, thus a single lineage of active families has evolved in this group. In contrast, non-mammalian genomes (fish, amphibians, reptiles) harbor a large diversity of concurrently transposing families, which are all represented by very small number of recently inserted copies. Why the pattern of diversity and abundance of L1 is so different among vertebrates remains unknown. To address this …

Evolutionary Interpretations Of Mycobacteriophage Biodiversity And Host-Range Through The Analysis Of Codon Usage Bias, Laura A. Esposito, Swati Gupta, Fraida Streiter, Ashley Prasad, John J. Dennehy

Publications and Research

In an genomics course sponsored by the Howard Hughes Medical Institute (HHMI), undergraduate students have isolated and sequenced the genomes of more than 1,150 mycobacteriophages, creating the largest database of sequenced bacteriophages able to infect a single host, Mycobacterium smegmatis, a soil bacterium. Genomic analysis indicates that these mycobacteriophages can be grouped into 26 clusters based on genetic similarity. These clusters span a continuum of genetic diversity, with extensive genomic mosaicism among phages in different clusters. However, little is known regarding the primary hosts of these mycobacteriophages in their natural habitats, nor of their broader host ranges. As such, it …

A Species-Level Phylogeny Of Extant Snakes With Description Of A New Colubrid Subfamily And Genus, Alex Figueroa, Alexander D. Mckelvy, L. Lee Grismer, Charles D. Bell, Simon P. Lailvaux

Publications and Research

Background With over 3,500 species encompassing a diverse range of morphologies and ecologies, snakes make up 36% of squamate diversity. Despite several attempts at estimating higherlevel snake relationships and numerous assessments of generic- or species-level phylogenies, a large-scale species-level phylogeny solely focusing on snakes has not been completed. Here, we provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61).

Results Increased taxon sampling resulted …

Biodiversity Of Medicinal Plants In The Highlands: Problems And Perspectives, Vyacheslav Dushenkov

Publications and Research

Climate change is affecting medicinal plants around the world and could ultimately lead to losses of some key species, in particular species endemic to a region and causing plants to migrate to new ranges. As the situation unfolds, climate change may become a pressing issue for the herbal community, affecting medicinal plant supply chains with varying requirements for plant cultivation, resource management in the wild, harvesting, processing, and importantly marketing.

Potyviral Genome-Linked Protein And Its Interaction With Plant Defense Ribosome Inactivating Protein From Phytolacca Americana, Artem V. Domashevskiy

Publications and Research

Agriculture is an indispensable part of every person’s life, ensuring that nutritious and inexpensive food is readily available. Agriculture continues to be confronted with epidemics, having devastating effects on economies and the plant sources essential for human and animal life. Plants and their pathogens have developed evolutionary adaptations, each shaping the other’s defence and invasive strategies. Many different plants produce toxic ribosome inactivating proteins that aid in their defence mechanisms against pathogenic invaders. Viruses must adapt to the host translational machinery, several having evolved to include viral genome-linked proteins that carry numerous viral functions. Here, we review how a potyviral …

Molecular Tracking Of Individual Host Use In The Shiny Cowbird – A Generalist Brood Parasite, Ma Alicia De La Colina, Mark E. Hauber, Bill M. Strausberger, Juan Carlos Reboreda, Bettina Mahler

Publications and Research

Generalist parasites exploit multiple host species at the population level, but the individual parasite’s strategy may be either itself a generalist or a specialist pattern of host species use. Here, we studied the relationship between host availability and host use in the individual parasitism patterns of the Shiny Cowbird Molothrus bonariensis, a generalist avian obligate brood parasite that parasitizes an extreme range of hosts. Using five microsatellite markers and an 1120-bp fragment of the mtDNA control region, we reconstructed full-sibling groups from 359 cowbird eggs and chicks found in nests of the two most frequent hosts in our study area, …

Bathymetric Survey For Lakes Azuei And Enriquillo, Hispaniola, Michael Piasecki, Mahrokh Moknatian, Fred Moshary, Joseph Cleto, Yolanda Leon, Jorge Gonzalez, Daniel Comarazamy

Publications and Research

The two largest lakes on the Caribbean Island of Hispaniola, Lake Azuei in Haiti and Lake Enriquillo in the Dominican Republic, have experienced dramatic growth and surface area expansion over the past few years leading to severe flooding and loss of arable land around the lake perimeters. In order to better understand the reasons for this unprecedented rate of expansion and the resulting consequences a multi-disciplinary team comprised of researchers from Haiti, the DR, and the US have embarked on an extensive data collecting and hydrologic and climatological modeling campaign. While the sensor deployment entails stations that measure climatological data …

Dynamic Egg Color Mimicry, Daniel Hanley, Michael Sulc, Patricia L. R. Brennan, Mark E. Hauber, Tomas Grim, Marcel Honza

Publications and Research

Evolutionary hypotheses regarding the function of eggshell phenotypes, from solar protection through mimicry, have implicitly assumed that eggshell appearance remains static throughout the laying and incubation periods. However, recent research demonstrates that egg coloration changes over relatively short, biologically relevant timescales. Here, we provide the first evidence that such changes impact brood parasite–host eggshell color mimicry during the incubation stage. First, we use long-term data to establish how rapidly the Acrocephalus arundinaceus Linnaeus (great reed warbler) responded to natural parasitic eggs laid by the Cuculus canorus Linnaeus (common cuckoo). Most hosts rejected parasitic eggs just prior to clutch completion, but …

Comparative Genomics Explains The Evolutionary Success Of Reef-Forming Corals, Debashish Bhattacharya, Shobhit Agrawal, Manuel Aranda, Sebastian Baumgarten, Mahdi Belcaid, Jeana L. Drake, Douglas Erwin, Sylvian Foret, Ruth D. Gates, David F. Gruber, Bishoy Kamel, Michael P. Lesser, Oren Levy, Yi Jin Liew, Matthew Macmanes, Tali Mass, Monica Medina, Shaadi Mehr, Eli Meyer, Dana C. Price, Hollie M. Putnam, Huan Qiu, Chuya Shinzato, Eiichi Shoguchi, Alexander J. Stokes, Sylvie Tambutté, Dan Tchernov, Christian R. Voolstra, Nicole Wagner, Charles W. Walker, Andreas Pm Weber, Virginia Weis, Ehud Zelzion, Didier Zoccola, Paul G. Falkowski

Publications and Research

Transcriptome and genome data from twenty stony coral species and a selection of reference bilaterians were studied to elucidate coral evolutionary history. We identified genes that encode the proteins responsible for the precipitation and aggregation of the aragonite skeleton on which the organisms live, and revealed a network of environmental sensors that coordinate responses of the host animals to temperature, light, and pH. Furthermore, we describe a variety of stress-related pathways, including apoptotic pathways that allow the host animals to detoxify reactive oxygen and nitrogen species that are generated by their intracellular photosynthetic symbionts, and determine the fate of corals …

Biofluorescence In Catsharks (Scyliorhinidae): Fundamental Description And Relevance For Elasmobranch Visual Ecology, David F. Gruber, Ellis R. Loew, Dimitri D. Deheyn, Derya Akkaynak, Jean P. Gaffney, W. Leo Smith, Matthew P. Davis, Jennifer H. Stern, Vincent A. Pieribone, John S. Sparks

Publications and Research

Biofluorescence has recently been found to be widespread in marine fishes, including sharks. Catsharks, such as the Swell Shark (Cephaloscyllium ventriosum) from the eastern Pacific and the Chain Catshark (Scyliorhinus retifer) from the western Atlantic, are known to exhibit bright green fluorescence. We examined the spectral sensitivity and visual characteristics of these reclusive sharks, while also considering the fluorescent properties of their skin. Spectral absorbance of the photoreceptor cells in these sharks revealed the presence of a single visual pigment in each species. Cephaloscyllium ventriosum exhibited a maximum absorbance of 484 ± 3 nm and an absorbance range at half …

Diversity-Dependent Cladogenesis Throughout Western Mexico: Evolutionary Biogeography Of Rattlesnakes (Viperidae: Crotalinae: Crotalus And Sistrurus), Christopher Blair, Santiago Sánchez-Ramírez

Publications and Research

Rattlesnakes (Crotalus and Sistrurus) represent a radiation of approximately 42 species distributed throughout the New World from southern Canada to Argentina. Interest in this enigmatic group of snakes continues to accrue due, in part, to their ecomorphological diversity, contributions to global envenomations, and potential medicinal importance. Although the group has garnered substantial attention from systematists and evolutionary biologists for decades, little is still known regarding patterns of lineage diversification. In addition, few studies have statistically quantified broad-scale biogeographic patterns in rattlesnakes to ascertain how dispersal occurred throughout the New World, particularly among the different major biomes of the …

Review Paper: The Shape Of Phylogenetic Treespace, Katherine St. John

Publications and Research

Trees are a canonical structure for representing evolutionary histories. Many popular criteria used to infer optimal trees are computationally hard, and the number of possible tree shapes grows super-exponentially in the number of taxa. The underlying structure of the spaces of trees yields rich insights that can improve the search for optimal trees, both in accuracy and in running time, and the analysis and visualization of results. We review the past work on analyzing and comparing trees by their shape as well as recent work that incorporates trees with weighted branch lengths.

Eggshell Pigment Composition Covaries With Phylogeny, Kaat Brulez, Ivan Miksik, Christopher R. Cooney, Mark E. Hauber, Paul George Lovell, Golo Maurer, Steven J. Portugal, Douglas Russell, Silas James Reynolds, Phillip Cassey

Publications and Research

No single hypothesis is likely to explain the diversity in eggshell coloration and patterning across birds, suggesting that eggshell appearance is most likely to have evolved to fulfill many nonexclusive functions. By controlling for nonindependent phylogenetic associations between related species, we describe this diversity using museum eggshells of 71 British breeding passerine species to examine how eggshell pigment composition and concentrations vary with phylogeny and with life-history and nesting ecology traits. Across species, concentrations of biliverdin and protoporphyrin, the two main pigments found in eggshells, were strongly and positively correlated, and both pigments strongly covaried with phylogenetic relatedness. Controlling for …

Editorial: Systems Biology And Ecology Of Microbial Mat Communities, Martin G. Klotz, Donald A. Bryant, Jim K. Fredrickson, William P. Inskeep, Michael Kühl

Publications and Research

No abstract provided.

Are We Overestimating The Niche? Removing Marginal Localities Helps Ecological Niche Models Detect Environmental Barriers, Mariano Soley-Guardia, Eliécer E. Gutiérrez, Darla M. Thomas, José Ochoa-G, Marisol Aguilera, Robert P. Anderson

Publications and Research

Correlative ecological niche models (ENMs) estimate species niches using occurrence records and environmental data. These tools are valuable to the field of biogeography, where they are commonly used to infer potential connectivity among populations. However, a recent study showed that when locally relevant environmental data are not available, records from patches of suitable habitat protruding into otherwise unsuitable regions (e.g., gallery forests within dry areas) can lead to overestimations of species niches and their potential distributions. Here, we test whether this issue obfuscates detection of an obvious environmental barrier existing in northern Venezuela – that of the hot and xeric …

Comparative Phylogeography Of Ethiopian Anurans: Impact Of The Great Rift Valley And Pleistocene Climate Change, Xenia Freilich, Jose D. Anadon, Jolanta Bukala, Ordaliza Calderon, Ronveer Chakraborty, Stephanie Boissinot

Publications and Research

Background: The Ethiopian highlands are a biodiversity hotspot, split by the Great Rift Valley into two distinct systems of plateaus and mountains. The Rift Valley is currently hot and dry and acts as a barrier to gene flow for highland-adapted species. It is however unlikely that the conditions in the Rift were inhospitable to highland species during the entire Pleistocene. To assess the significance of the Ethiopian Rift as a biogeographic barrier as well as the impact Pleistocene climatic changes have had on the evolution of Ethiopian organisms, we performed phylogeographic analyses and developed present and past niche models on …